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package biofilter.util;

/**
 * Interface for classes that represent a mapping to a sequence.
 * @author t9i, Daniel Quest
 */
public interface MappedPosition {

    /**
     * Gets the start position of where the sequence mapped to a reference.
     *
     * @return
     */
    public int getStart();

    /**
     * Gets the last position of where the sequence mapped to a reference
     * @return
     */
    public int getEnd();

   /**
    * Gets the length of the read mapped
    */
    public int length();
    
    /**
     * Returns a character representation of the strand. +, -, .
     * @return
     */
    public char getStrand();

    /**
     * Gets a weight for the region mapped.  This could be an alignment score, a probability value or an experementally determined value.
     */
    public double getWeight();

    /**
     * get the query ID (usually a fasta header) for a search sequence
     */
    public String getQueryID();

    /**
     * get the subject ID for a database sequence hit by the query in the search
     */
    public String getSubjectID();

}
